galaxyproject / galaxyproject/idc
Add mocked DB (226) for gtdb-tk to CVMFS
- Dominant language
- Shell
- Stars
- 10
- Forks
- 8
- PR merge metrics
- No merged PRs in 30d
Description
This IWC wf fails since gtdb-tk DB is too big so memory fails in the github CI: https://github.com/galaxyproject/iwc/pull/1168
Can we upload the mock DB for 226 gtdb in CVMFS: https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/gtdbtk_package/mockup_db/mockup.tar.gz
It can be installed from the latest gtdb DM: https://github.com/galaxyproject/tools-iuc/blob/main/data_managers/data_manager_gtdbtk_database_installer/data_manager/gtdbtk_database_installer.xml
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by reviewing the failing IWC workflow in PR 1168 and the linked gtdbtk database manager installer XML. Inspect how the gtdb-tk 226 mockup.tar.gz source is installed and how reference data is published to CVMFS. Done means the mock database is available through CVMFS and the workflow no longer fails from the full database exceeding GitHub CI memory.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- github, shell
- Domain
- ci-cd, databases, infrastructure
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100